Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase.

By Y. Buganim, Dina A. Faddah, A. Cheng, É. Itskovich, S. Markoulaki, Kibibi Ganz, Sandy L. Klemm, Alexander van Oudenaarden, R. Jaenisch. Cell, 2012

857 citations recorded by the source corpus.

Subfields: Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c02f6b645d7c1c51da70d9fa77ddc82108266093

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Citations in the corpus

Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “, 2012a), where special bottleneck proteins may play a pivotal role (Buganim et al., 2012).”
In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming (2016, neutral): “Cellular reprogramming to pluripotency by forced expression of the Yamanaka factors ( Oct4, Sox2, Klf4, and c-Myc [OSKM]) occurs through the global remodeling of epigenetic marks (Buganim et al., 2012, 2013; Hansson et al., 2012; Polo et al., 2012).”
Identification of cell types from single-cell transcriptomes using a novel clustering method (2015, background): “However, the high variability in gene expression levels even between cells of the same type (Buganim et al. , 2012; Guo et al. , 2010; Hashimshony et al. , 2012; Shalek et al. , 2013) can confound this seemly straightforward clustering approach.”
Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages (2013, background): “[6] considered a measure of Jensen-Shannon Divergence (Figures 2C, D in their paper) with a similar idea in mind.”
Defining cell types and states with single-cell genomics (2015, background): “SeqFISH and MERFISH are combinatorial fluorescence in situ hybridization strategies that use successive rounds of labeling, imaging, and photobleaching to recover mRNA abundances and subcellular localization simultaneously (Lubeck and Cai 2012; Chen et al. 2015).”
Diffusion maps for high-dimensional single-cell analysis of differentiation data (2015, methodology): “Thus it has to be proven with dedicated biological experiments (e.g. as used by Buganim et al. (2012) and Takahashi and Yamanaka (2006)) whether the data is biologically ergodic or not. ref. methodology linear/ non- linear structure faithfulness robustness to noise / density heterogeneities no. of…”
Facilitators and Impediments of the Pluripotency Reprogramming Factors’ Initial Engagement with the Genome (2012, positive): “Interestingly, gene ontology reveals late genes that are required for pluripotency, such as NANOG, DPPA4, SOX2, GDF3, and PRDM14 (Buganim et al., 2012) within OSKM- DBRs, along with many others required for cell differentiation (Table S4).”
The Sox Family of Transcription Factors: Versatile Regulators of Stem and Progenitor Cell Fate (2013, neutral): “In general, overexpression of any of the SoxB1 factors promotes CNS progenitor cell proliferation, whereas depletion of these factors induces cell-cycle exit and onset of differentiation (Bylund et al., 2003; Cavallaro et al., 2008; Ferri et al., 2004; Graham et al., 2003; Kishi et al., 2000; Miyagi”